Models of the evolution of other aspects of languages, including phonology, remain scarce, even though this aspect of the data is also highly informative of language history. [1]} describe a method to infer cognates automatically, but this is done independently from the inference of the phylogeny; [2]} reconstruct phonological changes, but their method requires a previously reconstructed phylogeny as input. In a similar vein, Machine Learning algorithms have been applied to the task of cognate prediction, which proposes a plausible form for a word in a language based on related languages; see [3]} and the recent survey by [4]}. These works do not attempt to jointly infer the phylogeny of the languages.
